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jvs:fscan:manual:chapter2:physio

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jvs:fscan:manual:chapter2:physio [2011/03/31 14:49]
127.0.0.1 external edit 		jvs:fscan:manual:chapter2:physio [2023/02/23 18:43] (current)
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 **fScan Reference Manual, Chapter 2 (CmdLineOptions): pysio** **fScan Reference Manual, Chapter 2 (CmdLineOptions): pysio**
 ===== Physio -- Analyze physiological waveforms ===== ===== Physio -- Analyze physiological waveforms =====
-**usage:** -physio data flag [NAME val NAME2 val2 ...]+**usage:** -physio data flag [OPTNAME val OPTNAME2 val2 ...]
  
 ===== ===== ===== =====
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   * 2 list text files - specifying amplitude and time values separately   * 2 list text files - specifying amplitude and time values separately
   * 2 'pd' records - specifying records in a CIGAL 'pdigm' file for amplitude and time values   * 2 'pd' records - specifying records in a CIGAL 'pdigm' file for amplitude and time values
-  + 
 +The output of PHYSIO is one or more reference time course variables. 
 The FLAG argument specifies what should be done The FLAG argument specifies what should be done
   * FLAG - (values above 7 can be combined by addition)   * FLAG - (values above 7 can be combined by addition)
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     * 7 - pupilaspect     * 7 - pupilaspect
     * 010 - identify peak values     * 010 - identify peak values
-    * 020 - +    * 020 - identify trough values 
-    * 040 -+    * 040 - identify zero crossings (050-rising, 060-falling)
     * 0100 - generate resampled phase values     * 0100 - generate resampled phase values
     * 0200 - generate resampled rate values     * 0200 - generate resampled rate values
     * 0400 - generate resampled amplitude values     * 0400 - generate resampled amplitude values
-    * 01000 - +    * 01000 - calculate the amplitude range 
-    * 02000 - +
-    * 04000 -+
     * 010000 - flip X/Y axes     * 010000 - flip X/Y axes
  
-Additional options can be specified as 2-argument pairs of the form OPTION VALUE, where OPTION is the name of the option and VALUE is the value you want to assign for that option.  The recognized option names are:+Additional options can be specified as 2-argument pairs of the form, OPTNAME VALUE, where OPTNAME is the name of the option and VALUE is the value you want to assign for that option.  The recognized option names are:
   * bin -   * bin -
   * width -   * width -
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   * tr - scan TR time (sec per volume of images)   * tr - scan TR time (sec per volume of images)
   * nz - number of slices per TR   * nz - number of slices per TR
-  * interleave - slice timeing flag: 0=sequential, 1=odd then even, 2=even then odd (1st slice# = 1)+  * interleave - slice timing flag: 0=sequential, 1=odd then even, 2=even then odd (1st slice# = 1) (default from data hdr)
   * print - control output display options (default printing is to file 'physio_name.txt')   * print - control output display options (default printing is to file 'physio_name.txt')
     * 1 - print one-line summary      * 1 - print one-line summary 
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     * 4 - print resampled phase, rate, amplitude values     * 4 - print resampled phase, rate, amplitude values
     * 8 - print to standard output rather than default data file      * 8 - print to standard output rather than default data file 
 +    * 16 - print RETROICOR parameters
 +    * 32 - print RHVRCOR parameters
 +    * 64 - omit the column header line
 +  * range - with no argument, means just report percent signal fluctuation range
 +  * range - with a number argument, minimum percent signal range needed for physio analysis (default: 2 %) 
  
 **Examples:**\\ **Examples:**\\
jvs/fscan/manual/chapter2/physio.1301582953.txt.gz · Last modified: 2014/08/04 16:03 (external edit)

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